Changes in gene expression related to human development and related to development of cancer (tumorigenesis) are regulated by changes in the organization of chromatin. These mechanisms differ from gene mutations which occur by changes in the primary DNA sequence, and as a class are called epigenetic mechanisms of regulation. Genome-wide or global changes in nuclear organization occur during differentiation of human embryonic stem cells, both causing and signaling changes in cell function.
Genome-specific methods using arrays or PCR are common methods for determining genetic and, recently, epigenetic changes in specific genes. Gene-specific activity can be measured using genome wide arrays, and expression of specific markers can be detected by PCR. Unfortunately, these methods do not by themselves indicate nuclear organization. Imaging techniques have been used extensively in developmental biology and cancer pathophysiology, validating the general imaging approach. There is a need for quantitative measurement techniques and specific molecular markers of genome-wide organization in intact cells.